DNA microarray technology has been applied to many areas such as gene expression and discovery, mutation detection, allelic and evolutionary sequence comparison, genome mapping and more. Unfortunately, most applications fail to tap into the full capacity of microarray technology as many hybridization assays involve far less probes than are available using the full capability of the number of features possible in a high-density microarray.
The advent of DNA microarray technology makes it possible to build an array of hundreds of thousands of DNA sequences in a very small area, such as the size of a microscopic slide. See, e.g., U.S. Pat. No. 6,375,903 and U.S. Pat. No. 5,143,854, each of which is hereby incorporated by reference in its entirety. The disclosure of U.S. Pat. No. 6,375,903 enables the construction of so-called maskless array synthesizer (MAS™) instruments in which light is used to direct synthesis of the DNA sequences, the light direction being performed using a digital micromirror device (DMD). Using an MAS™ instrument, the selection of DNA sequences to be constructed in the microarray is under software control so that individually customized arrays can be built to order. In general, MAS™ based DNA microarray synthesis technology allows for the parallel synthesis of over 800,000 unique oligonucleotides in a very small area of on a standard microscope slide. For many applications, the entirety of the synthesized array is devoted to the evaluation of one sample of test nucleic acids (i.e., RNA or DNA). In these applications, the entire microarray area is enclosed in a small chamber so as to allow for the application of the single sample, thus providing a very efficient means for measuring the concentration of a very large number of nucleic acid molecules within that one sample. A typical application of this sort is gene expression profiling.
In applications where a smaller number of genes are being studied, or where a reduced set of probes will be queried for each sample, the microarray can be logically divided into any number of smaller arrays (i.e., subarrays) each having the same or different nucleotide probes, a concept sometimes referred to as an array of arrays. To use an array of arrays efficiently, multiple samples are hybridized in parallel, in a single experiment, with each sample being hybridized to a given and known subarray in the array of arrays. This parallel loading strategy provides for efficient utilization of the high synthesis capacity of the microarray. In order to load multiple samples onto an array or an array of arrays and avoid sample cross-contamination, some mechanism must be provided to sequester each sample from adjacent samples. Currently, microarrays built for this purpose (e.g., U.S. Pat. No. 5,874,219) use physical wells to separate probe sets for different samples. This approach, however, requires the user to know precisely where the array has been synthesized on the slide in order to properly place the barriers forming the well walls. Alternatively, the user could compensate for the ambiguity by reducing the dimensions of the subarrays in order to allow for error in barrier placement. This is not an ideal approach since it wastes synthetic capacity in the interest of enclosing a full experimental set of features within each subarray.